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pyproject.toml
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pyproject.toml
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[tool.poetry]
name = "micone"
version = "0.15.0"
description = "The Microbial Co-occurrence Network Explorer"
authors = ["Dileep Kishore <[email protected]>"]
license = "MIT"
readme = "README.md"
homepage = "https://github.com/segrelab/MiCoNE"
documentation = "https://micone.readthedocs.io/en/latest"
[tool.poetry.dependencies]
python = ">=3.11"
numpy = "^1.19.4"
pandas = "^1.2.0"
biom-format = "^2.1.10"
h5py = "^3.1.0"
ete3 = "^3.1.2"
statsmodels = "0.14.0"
networkx = "^2.5"
schematics = "^2.1.0"
halo = "^0.0.31"
loguru = "^0.5.3"
Jinja2 = "^2.11.2"
jinja2schema = "^0.1.4"
matplotlib = "^3.3.3"
simplejson = "^3.17.2"
markupsafe = "2.0.1"
Sphinx = "^5.1.1"
sphinx-rtd-theme = "^1.0.0"
click = "^8.1.3"
[tool.poetry.dev-dependencies]
flake8 = "^3.8.4"
coverage = {extras = ["toml"], version = "^5.3.1"}
pytest = "^7.2.0"
ipython = "^8.15.0"
pylint = "^2.6.0"
pre-commit = "^2.9.3"
pytest-cov = "^2.11.0"
black = "^23.3.0"
[tool.poetry.extras]
docs = ["Sphinx", "sphinx-rtd-theme"]
[tool.poetry.group.dev.dependencies]
sourcery = "^1.8.0"
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
[tool.coverage.run]
branch = true
source = ["micone"]
[tool.coverage.report]
exclude_lines = [
"if self.debug:",
"pragma: no cover",
"raise NotImplementedError",
"if __name__ == .__main__.:",
]
ignore_errors = true
omit = [
"tests/*",
"micone/pipelines/envs/*",
"micone/pipelines/src/*",
]
[tool.poetry.scripts]
micone = "micone.cli:main"